tbuckley/cabot-search huggingface dataset:
Imported spring onions related to the first recorded outbreak of enteroinvasive Escherichia coli in Denmark, November to December 2021
Authors: Mia Torpdahl, Emily Dibba White, Susanne Schjørring, Malene Søby, Jørgen Engberg, Anne Line Engsbro, Hanne M Holt, Lars Lemming, Lisbeth Lützen, Bente Olesen, John E Coia, Charlotte Kjelsø, Luise Müller
Journal: Eurosurveillance (2023)

Between November and December 2021, the first ever recorded outbreak of enteroinvasive Escherichia coli in Denmark occurred at national scale. We describe the investigation of this outbreak, which was initially recognised in early December 2021. A total of 88 cases (58 female; 30 male) with a median age of 52 years (range: 0-91) were detected by PCR-based diagnostic methods. Case ascertainment was complicated by current culture-free diagnostic procedures, with only 34 cases confirmed by culture, serotyping and whole genome sequencing. Isolates from cases grouped into two serotypes (O136:H7 and O96:H19), which was supported by whole-genome-sequence-phylogeny, also yielding two clusters. Interviews of 42 cases and traceback investigation pointed towards consumption of ready-to-eat salads as the outbreak cause. While the ready-to-eat salads comprised different vegetables, imported spring onions were the only common ingredient and thus the likely source. Environmental investigations failed to recover outbreak strains. This report highlights the value of fast typing (here O-typing) to confirm cases in an outbreak situation. Timely communication and data sharing are also important, and were facilitated by the national collaboration between relevant laboratories, the public health institute and the veterinary and food administration. High hygiene standards for imported fresh vegetables intended for ready-to-eat products are essential.
Population-Based Cholesterol Screening as a Primordial Prevention Strategy—Breaking the Cycle of Adverse Lipid Levels That Runs in Families and Tracks Through Life
Authors: Jacob J. Christensen, Kirsten B. Holven
Journal: JAMA Network Open (2023)

Ursa Sustar, MSc; Olga Kordonouri, MD, PhD; Stefan Arens, MD; Jernej Kovac, PhD; Katarina Sedej, MD, PhD; Tadej Battelino, MD, PhD; Urh Groselj, MD, PhD, MA
Adaptive Evolution of the Spike Protein in Coronaviruses
Authors: Xiaolu Tang, Zhaohui Qian, Xuemei Lu, Jian Lu
Journal: Molecular Biology and Evolution (2023)

Abstract Coronaviruses are single-stranded, positive-sense RNA viruses that can infect many mammal and avian species. The Spike (S) protein of coronaviruses binds to a receptor on the host cell surface to promote viral entry. The interactions between the S proteins of coronaviruses and receptors of host cells are extraordinarily complex, with coronaviruses from different genera being able to recognize the same receptor and coronaviruses from the same genus able to bind distinct receptors. As the coronavirus disease 2019 pandemic has developed, many changes in the S protein have been under positive selection by altering the receptor-binding affinity, reducing antibody neutralization activities, or affecting T-cell responses. It is intriguing to determine whether the selection pressure on the S gene differs between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronaviruses due to the host shift from nonhuman animals to humans. Here, we show that the S gene, particularly the S1 region, has experienced positive selection in both SARS-CoV-2 and other coronaviruses. Although the S1 N-terminal domain exhibits signals of positive selection in the pairwise comparisons in all four coronavirus genera, positive selection is primarily detected in the S1 C-terminal domain (the receptor-binding domain) in the ongoing evolution of SARS-CoV-2, possibly owing to the change in host settings and the widespread natural infection and SARS-CoV-2 vaccination in humans.
Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization
Authors: Sibelle T Vilaça, Michael E Donaldson, Andrea Benazzo, Tyler J Wheeldon, Maria Teresa Vizzari, Giorgio Bertorelle, Brent R Patterson, Christopher J Kyle
Journal: Molecular Biology and Evolution (2023)

Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between "western" coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada.
Nonhealing Cutaneous Ulcers in a Patient With Myelodysplastic Syndrome
Authors: Aryanna I. Jordan, Ling Zhang, Seongseok Yun
Journal: JAMA Oncology (2023)

A 75-year-old man with myelodysplastic syndrome that has been well controlled with lenalidomide develops multiple nonhealing cutaneous ulcers. What is your diagnosis?
Reactive Oxygen Species‐Scavenging Nanosystems in the Treatment of Diabetic Wounds
Authors: Yuan Xiong, Xiangyu Chu, Tao Yu, Samuel Knoedler, Andreas Schroeter, Li Lu, Kangkang Zha, Ze Lin, Dongsheng Jiang, Yuval Rinkevich, Adriana C. Panayi, Bobin Mi, Guohui Liu, Yanli Zhao
Journal: Advanced Healthcare Materials (2023)

Diabetic wounds are characterized by drug-resistant bacterial infections, biofilm formation, impaired angiogenesis and perfusion, and oxidative damage to the microenvironment. Given their complex nature, diabetic wounds remain a major challenge in clinical practice. Reactive oxygen species (ROS), which have been shown to trigger hyperinflammation and excessive cellular apoptosis, play a pivotal role in the pathogenesis of diabetic wounds. ROS-scavenging nanosystems have recently emerged as smart and multifunctional nanomedicines with broad synergistic applicability. The documented anti-inflammatory and pro-angiogenic ability of ROS-scavenging treatments predestines these nanosystems as promising options for the treatment of diabetic wounds. Yet, in this context, the therapeutic applicability and efficacy of ROS-scavenging nanosystems remain to be elucidated. Herein, the role of ROS in diabetic wounds is deciphered, and the properties and strengths of nanosystems with ROS-scavenging capacity for the treatment of diabetic wounds are summarized. In addition, the current challenges of such nanosystems and their potential future directions are discussed through a clinical-translational lens.
A third vaccine dose equalises the levels of effectiveness and immunogenicity of heterologous or homologous COVID-19 vaccine regimens, Lyon, France, December 2021 to March 2022
Authors: Nicolas Guibert, Kylian Trepat, Bruno Pozzetto, Laurence Josset, Jean-Baptiste Fassier, Omran Allatif, Kahina Saker, Karen Brengel-Pesce, Thierry Walzer, Philippe Vanhems, Sophie Trouillet-Assant
Journal: Eurosurveillance (2023)

Background To cope with the persistence of the COVID-19 epidemic and the decrease in antibody levels following vaccination, a third dose of vaccine has been recommended in the general population. However, several vaccine regimens had been used initially for the primary vaccination course, and the heterologous Vaxzevria/Comirnaty regimen had shown better efficacy and immunogenicity than the homologous Comirnaty/Comirnaty regimen. Aim We wanted to determine if this benefit was retained after a third dose of an mRNA vaccine. Methods We combined an observational epidemiological study of SARS-CoV-2 infections among vaccinated healthcare workers at the University Hospital of Lyon, France, with a prospective cohort study to analyse immunological parameters before and after the third mRNA vaccine dose. Results Following the second vaccine dose, heterologous vaccination regimens were more protective against infection than homologous regimens (adjusted hazard ratio (HR) = 1.88; 95% confidence interval (CI): 1.18–3.00; p = 0.008), but this was no longer the case after the third dose (adjusted HR = 0.86; 95% CI: 0.72–1.02; p = 0.082). Receptor-binding domain-specific IgG levels and serum neutralisation capacity against different SARS-CoV-2 variants were higher after the third dose than after the second dose in the homologous regimen group, but not in the heterologous group. Conclusion The advantage conferred by heterologous vaccination was lost after the third dose in terms of both protection and immunogenicity. Immunological measurements 1 month after vaccination suggest that heterologous vaccination induces maximal immunity after the second dose, whereas the third dose is required to reach the same level in individuals with a homologous regimen.
The association between cognitive ability and body mass index: A sibling-comparison analysis in four longitudinal studies
Authors: Liam Wright, Neil M. Davies, David Bann
Journal: PLoS Medicine (2023)

Body mass index (BMI) and obesity rates have increased sharply since the 1980s. While multiple epidemiologic studies have found that higher adolescent cognitive ability is associated with lower adult BMI, residual and unobserved confounding due to family background may explain these associations. We used a sibling design to test this association accounting for confounding factors shared within households.
Erratum. The Association of Measures of Cardiovascular Autonomic Function, Heart Rate, and Orthostatic Hypotension With Incident Glucose Disorders: The Cardiovascular Health Study. Diabetes Care 2022;45:2376–2382
Authors: Joshua I. Barzilay, William Tressel, Mary L. Biggs, Phyllis K. Stein, Jorge R. Kizer, Sanyog G. Shitole, Yakubu Bene-Alhasan, Kenneth J. Mukamal
Journal: Diabetes Care (2023)

In Table 3 of the article cited above, the β (95% CI) and P value data were incorrect due to a calculation error. The revised data do not identify specific associations of measures of autonomic function with fasting measures of insulin resistance or insulin secretion available in the Cardiovascular Health Study (CHS). However, the main outcome of the article—that certain measures of cardiac autonomic function are prospectively associated with fasting glucose level changes—remains unaffected.
Health Care–Associated Infections Among Hospitalized Patients With COVID-19, March 2020-March 2022
Authors: Kenneth E. Sands, E. Jackie Blanchard, Sarah Fraker, Kimberly Korwek, Michael Cuffe
Journal: JAMA Network Open (2023)

The reported incidence of many health care-associated infections (HAIs) increased during the COVID-19 pandemic; however, it is unclear whether this is due to increased patient risk or to increased pressure on the health care system.To assess HAI occurrence among patients admitted to hospitals with and without COVID-19.A cross-sectional retrospective analysis of inpatients discharged both with and without laboratory-confirmed COVID-19 infection was conducted. Data were obtained between January 1, 2019, and March 31, 2022, from community hospitals affiliated with a large health care system in the US.COVID-19 infection.Occurrence of central line-associated bloodstream infection (CLABSI), catheter-associated urinary tract infection (CAUTI), methicillin-resistant Staphylococcus aureus (MRSA) bacteremia, and Clostridioides difficile infection as reported to the National Healthcare Safety Network.Among nearly 5 million hospitalizations in 182 hospitals between 2020 and 2022, the occurrence of health care-associated infections (HAIs) was high among the 313 200 COVID-19 inpatients (median [SD] age, 57 [27.3] years; 56.0% women). Incidence per 100 000 patient-days showed higher HAIs among those with COVID-19 compared with those without. For CLABSI, the incidence for the full 9 quarters of the study was nearly 4-fold higher among the COVID-19 population than the non-COVID-19 population (25.4 vs 6.9). For CAUTI, the incidence in the COVID-19 population was 2.7-fold higher in the COVID-19 population (16.5 vs 6.1), and for MRSA, 3.0-fold higher (11.2 vs 3.7). Quarterly trends were compared with the same quarter in 2019. The greatest increase in the incidence of HAI in comparison with the same quarter in 2019 for the entire population occurred in quarter 3 of 2020 for CLABSI (11.0 vs 7.3), quarter 4 of 2021 for CAUTI (7.8 vs 6.8), and quarter 3 of 2021 for MRSA (5.2 vs 3.9). When limited to the non-COVID-19 population, the increase in CLABSI incidence vs the 2019 incidence was eliminated, and the quarterly rates of MRSA and CAUTI were lower vs the prepandemic 2019 comparator quarter.In this cross-sectional study of hospitals during the pandemic, HAI occurrence among inpatients without COVID-19 was similar to that during 2019 despite additional pressures for infection control and health care professionals. The findings suggest that patients with COVID-19 may be more susceptible to HAIs and may require additional prevention measures.
A case of <i>Paederus</i> dermatitis in Western Europe: a signal for a One Health–One World concept for the dermatologist
Authors: Alexis Descatha, Khaled Ezzedine, Gaël Le Roux
Journal: British Journal of Dermatology (2023)

This reported case of Paederus dermatitis in Western Europe materializes the concept of One Health–One World to dermatologists. Although the condition is benign, the dermatologist should be aware of the diagnosis of Paederus dermatitis as global warming may lead to its spread in Western countries.
Epidemiologic and Clinical Features of Mpox-Associated Deaths — United States, May 10, 2022–March 7, 2023
Authors: Aspen P. Riser, Allison Hanley, Michael Cima, Linda Lewis, Kayla Saadeh, Jemma Alarcón, Lauren Finn, Moon Kim, Jeremy Adams, Douglas Holt, Amanda Feldpausch, Jessica Pavlick, Andrew English, Marguerite Smith, Tyler Rehman, Ronald Lubelchek, Stephanie Black, Matthew Collins, Layne Mounsey, David Blythe, Meredith Hodach Avalos, Ellen H. Lee, Olivia Samson, Marcia Wong, B. Denise Stokich, Ellen Salehi, Lynn Denny, Kirsten Waller, Pamela Talley, Julie Schuman, Michael Fischer, Stephen White, Kenneth Davis, Ashley Caeser Cuyler, Rabeeya Sabzwari, Robert N. Anderson, Katrina Byrd, Jeremy A. W. Gold, Shannon Kindilien, James T. Lee, Siobhán O’Connor, Jesse O’Shea, LaTweika A. T. Salmon-Trejo, Raquel Velazquez-Kronen, Carla Zelaya, William Bower, Sascha Ellington, Adi V. Gundlapalli, Andrea M. McCollum, Leah Zilversmit Pao, Agam K. Rao, Karen K. Wong, Sarah Anne J. Guagliardo
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

As of March 7, 2023, a total of 30,235 confirmed and probable monkeypox (mpox) cases were reported in the United States,† predominantly among cisgender men§ who reported recent sexual contact with another man (1). Although most mpox cases during the current outbreak have been self-limited, cases of severe illness and death have been reported (2-4). During May 10, 2022-March 7, 2023, 38 deaths among persons with probable or confirmed mpox¶ (1.3 per 1,000 mpox cases) were reported to CDC and classified as mpox-associated (i.e., mpox was listed as a contributing or causal factor). Among the 38 mpox-associated deaths, 94.7% occurred in cisgender men (median age = 34 years); 86.8% occurred in non-Hispanic Black or African American (Black) persons. The median interval from symptom onset to death was 68 days (IQR = 50-86 days). Among 33 decedents with available information, 93.9% were immunocompromised because of HIV. Public health actions to prevent mpox deaths include integrated testing, diagnosis, and early treatment for mpox and HIV, and ensuring equitable access to both mpox and HIV prevention and treatment, such as antiretroviral therapy (ART) (5).
Wang D, Sun Z, Zhu X, et al. GARP-mediated active TGF-β1 induces bone marrow NK cell dysfunction in AML patients with early relapse post–allo-HSCT. <i>Blood.</i> 2022;140(26):2788-2804.
Authors: Dongyao Wang, Zimin Sun, Xiaoyu Zhu, Xiaohu Zheng, Yonggang Zhou, Yichen Lu, Peidong Yan, Huiru Wang, Huilan Liu, Jing Jin, Huaiping Zhu, Rui Sun, Yi Wang, Binqing Fu, Zhigang Tian, Haiming Wei
Journal: Blood (2023)
Update on Wild Poliovirus Type 1 Outbreak — Southeastern Africa, 2021–2022
Authors: Elizabeth Davlantes, Sharon A. Greene, Farrell A. Tobolowsky, Oladayo Biya, Eric Wiesen, Fikru Abebe, Mesfin B. Weldetsadik, Victor A. Eboh, Mike N. Chisema, Balbina da Conceição Mário, Florian Tinuga, Patricia Mupeta Bobo, Colline Koline Chigodo, Ghanashyam Sethy, Jan-Marcus Hellström, Abdou Moumouni Goundara, Marie-Eve Burny, Jonas C. Mwale, Jaume Jorba, Koketso S. Makua, Wayne Howard, Lerato Seakamela, Samuel Okiror, Andrea Thompson, Asma Ali, Dhoud Samba, Chukwuemeka Agbo, Lusamba Kabamba, Anthony Kazoka, Delayo Laurel Zomahoun, Fadinding Manneh, Khalid Abdelrahim, Chris Kamugisha, Abubakar Sadiq Umar
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Since the Global Polio Eradication Initiative (GPEI) began in 1988, the number of wild poliovirus (WPV) cases has declined by >99.99%. Five of the six World Health Organization (WHO) regions have been certified free of indigenous WPV, and WPV serotypes 2 and 3 have been declared eradicated globally (1). WPV type 1 (WPV1) remains endemic only in Afghanistan and Pakistan (2,3). Before the outbreak described in this report, WPV1 had not been detected in southeastern Africa since the 1990s, and on August 25, 2020, the WHO African Region was certified free of indigenous WPV (4). On February 16, 2022, WPV1 infection was confirmed in one child living in Malawi, with onset of paralysis on November 19, 2021. Genomic sequence analysis of the isolated poliovirus indicated that it originated in Pakistan (5). Cases were subsequently identified in Mozambique. This report summarizes progress in the outbreak response since the initial report (5). During November 2021-December 2022, nine children and adolescents with paralytic polio caused by WPV1 were identified in southeastern Africa: one in Malawi and eight in Mozambique. Malawi, Mozambique, and three neighboring countries at high risk for WPV1 importation (Tanzania, Zambia, and Zimbabwe) responded by increasing surveillance and organizing up to six rounds of national and subnational polio supplementary immunization activities (SIAs).* Although no cases of paralytic WPV1 infection have been reported in Malawi since November 2021 or in Mozambique since August 2022, undetected transmission might be ongoing because of poliovirus surveillance gaps and testing delays. Efforts to further enhance poliovirus surveillance sensitivity, improve SIA quality, and strengthen routine immunization are needed to ensure that WPV1 transmission has been interrupted within 12 months of the first case, thereby preserving the WHO African Region's WPV-free status.
Secondary Cases of Invasive Disease Caused by Encapsulated and Nontypeable <i>Haemophilus influenzae</i> — 10 U.S. Jurisdictions, 2011–2018
Authors: Sara E. Oliver, Amy B. Rubis, Heidi M. Soeters, Arthur Reingold, Meghan Barnes, Susan Petit, Ashley E. Moore, Lee H. Harrison, Ruth Lynfield, Kathy M. Angeles, Kari E. Burzlaff, Ann Thomas, William Schaffner, Henju Marjuki, Xin Wang, Susan Hariri
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Haemophilus influenzae (Hi) can cause meningitis and other serious invasive disease. Encapsulated Hi is classified into six serotypes (a-f) based on chemical composition of the polysaccharide capsule; unencapsulated strains are termed nontypeable Hi (NTHi). Hi serotype b (Hib) was the most common cause of bacterial meningitis in children in the pre-Hib vaccine era, and secondary transmission of Hi among children (e.g., to household contacts and in child care facilities) (1,2) led to the Advisory Committee on Immunization Practices (ACIP) recommendation for antibiotic chemoprophylaxis to prevent Hib disease in certain circumstances.* High Hib vaccination coverage since the 1990s has substantially reduced Hib disease, and other serotypes now account for most Hi-associated invasive disease in the United States (3). Nevertheless, CDC does not currently recommend chemoprophylaxis for contacts of persons with invasive disease caused by serotypes other than Hib and by NTHi (non-b Hi). Given this changing epidemiology, U.S. surveillance data were reviewed to investigate secondary cases of invasive disease caused by Hi. The estimated prevalence of secondary transmission was 0.32% among persons with encapsulated Hi disease (≤60 days of one another) and 0.12% among persons with NTHi disease (≤14 days of one another). Isolates from all Hi case pairs were genetically closely related, and all patients with potential secondary infection had underlying medical conditions. These results strongly suggest that secondary transmission of non-b Hi occurs. Expansion of Hi chemoprophylaxis recommendations might be warranted to control invasive Hi disease in certain populations in the United States, but further analysis is needed to evaluate the potential benefits against the risks, such as increased antibiotic use.
A multistep approach from scoping review to strong evidence: biomarkers in psoriasis
Authors: E Sbidian
Journal: British Journal of Dermatology (2023)

Journal Article A multistep approach from scoping review to strong evidence: biomarkers in psoriasis Get access E Sbidian E Sbidian UPEC EpiDermE, Inserm, Centre d’Investigation Clinique 1430, Department of Dermatology, AP-HP Hôpital Henri Mondor, 51 Avenue du Maréchal de Lattre de Tassigny, Créteil, 94000, France Correspondence: E. Sbidian. Email: Emilie.sbidian@aphp.fr https://orcid.org/0000-0002-1267-5270 Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 189, Issue 1, July 2023, Page e2, https://doi.org/10.1093/bjd/ljac101 Published: 13 April 2023 Article history Received: 24 October 2022 Revision received: 09 November 2022 Corrected and typeset: 13 April 2023 Published: 13 April 2023
Volume outcome relationship in postesophagectomy leak: a systematic review and meta-analysis
Authors: Mohamed Rahouma, Massimo Baudo, Nathan Mynard, Mohamed Kamel, Faiza M. Khan, Shon Shmushkevich, Kritika Mehta, Mohamed Hosny, Anas Dabsha, Sherif Khairallah, Michelle Demetres, Reda Saad, Abdelrahaman Mohamed, Jeffrey L. Port, Nasser K. Altorki, Mario Gaudino
Journal: International Journal of Surgery (2023)

Anastomotic leak after esophagectomy carries important short- and long-term sequelae. The authors conducted a systematic review and meta-analysis to determine its association with surgical volume.